FIGURE 2 | Building regulatory systems with transposable elements.

A family of DNA transposons is shown, with its multiple copies (white boxes) delimited by terminal inverted repeats (black triangles) and interspersed with genes (coloured boxes) in the genome. For panels a and b, the transposable element (TE) family could be also a retrotransposon family. a | Wiring of a transcriptional regulatory network by TE-derived cis-elements. A binding site for a DNA binding protein (DBP) has been dispersed throughout the genome as part of the TE. If the DBP is a transcription factor, its binding to a TE adjacent to a gene might influence the expression of that gene (solid arrows). Multiple genes are brought simultaneously under the control of the transcription factor through their association with different copies of the same TE family. b | Wiring of a post-transcriptional regulatory network by TE-derived cis-elements. Several TE copies are co-transcribed along with their neighbouring gene, resulting in the production of different mRNAs containing similar TEs (solid arrows). If the TE contains a binding site for an RNA-binding protein (RBP), it might engage the different mRNAs in the same post-transcriptional pathway of gene regulation. c | De novo assembly of a microRNA (miRNA) network from a TE family. This model combines the idea of TE and host gene co-transcription, as described in b, with the origin of a miRNA precursor containing a TE of the same family. This precursor could arise by transcription and intramolecular folding of a TE with a nearly perfect palindromic structure (for example, a miniature inverted repeat transposable element; MITE). The resulting double-stranded RNA could then be processed into a mature miRNA. The resulting TE-derived miRNA can pair with complementary TE sequences that are embedded within the 3' UTR of co-transcribed mRNAs. d | De novo assembly of cis and trans components of a transcriptional network from a DNA transposon family. In this model, the DBP is derived from a transposase (TPase), and therefore has the potential to bind to a network of sites previously distributed around the genome by related TEs. If the TPase-derived DBP has transcription-factor activity, it might regulate the expression of genes located in proximity to a binding site embedded within a related TE, including its own.

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